Fig. 1
From: Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
Path extension in Rcorrector. Four possible path continuations at the AGTC k-mer (k=4) in the De Bruijn graph for the r= AAGTCATAA read sequence. Numbers in the vertices represent k-mer counts. The first (top) path corresponds to the original read’s representation in the De Bruijn graph. The extension is pruned after the first step, AGTC →GTCA, as the count M(GTCA)=4 falls below the local cutoff (determined based on the maximum k-mer count (494) of the four possible successors of AGTC). The second path (yellow) has higher k-mer counts but it introduces four corrections, changing the read into AAGTCCGTC. The third path (blue) introduces only two corrections, to change the sequence into AAGTCGTTA, and is therefore chosen to correct the read. The fourth (bottom) path is pruned as the k-mer count for GTCT does not pass the threshold. Paths 2 and 3 are likely to indicate paralogs and/or splice variants of this gene